BioJava: an open-source framework for bioinformatics von Holland, R. C. G., Down, T. A., Pocock, M., Prlić, A., Huen, D., James, K., Foisy, S., Dräger, A., Yates, A., Heuer, M., Schreiber, M. J.

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Podbat: a novel genomic tool reveals Swr1-independent H2A.Z incorporation at gene coding sequences through epigenetic meta-analysis von Sadeghi, Laia, Bonilla, Carolina, Strålfors, Annelie, Ekwall, Karl, Svensson, J Peter

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BEAST 2: a software platform for Bayesian evolutionary analysis von Bouckaert, Remco, Heled, Joseph, Kühnert, Denise, Vaughan, Tim, Wu, Chieh-Hsi, Xie, Dong, Suchard, Marc A, Rambaut, Andrew, Drummond, Alexei J

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Software for computing and annotating genomic ranges von Lawrence, Michael, Huber, Wolfgang, Pagès, Hervé, Aboyoun, Patrick, Carlson, Marc, Gentleman, Robert, Morgan, Martin T, Carey, Vincent J

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ClonalFrameML: efficient inference of recombination in whole bacterial genomes von Didelot, Xavier, Wilson, Daniel J

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A toolbox for representational similarity analysis von Nili, Hamed, Wingfield, Cai, Walther, Alexander, Su, Li, Marslen-Wilson, William, Kriegeskorte, Nikolaus

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Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors von Serra, François, Baù, Davide, Goodstadt, Mike, Castillo, David, Filion, Guillaume J, Marti-Renom, Marc A

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CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures von Chovancova, Eva, Pavelka, Antonin, Benes, Petr, Strnad, Ondrej, Brezovsky, Jan, Kozlikova, Barbora, Gora, Artur, Sustr, Vilem, Klvana, Martin, Medek, Petr, Biedermannova, Lada, Sochor, Jiri, Damborsky, Jiri

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rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids von Ruiz-Carmona, Sergio, Alvarez-Garcia, Daniel, Foloppe, Nicolas, Garmendia-Doval, A Beatriz, Juhos, Szilveszter, Schmidtke, Peter, Barril, Xavier, Hubbard, Roderick E, Morley, S David

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SMOG 2: A Versatile Software Package for Generating Structure-Based Models von Noel, Jeffrey K, Levi, Mariana, Raghunathan, Mohit, Lammert, Heiko, Hayes, Ryan L, Onuchic, José N, Whitford, Paul C

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Chaste: an open source C++ library for computational physiology and biology von Mirams, Gary R, Arthurs, Christopher J, Bernabeu, Miguel O, Bordas, Rafel, Cooper, Jonathan, Corrias, Alberto, Davit, Yohan, Dunn, Sara-Jane, Fletcher, Alexander G, Harvey, Daniel G, Marsh, Megan E, Osborne, James M, Pathmanathan, Pras, Pitt-Francis, Joe, Southern, James, Zemzemi, Nejib, Gavaghan, David J

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Structure-derived substitution matrices for alignment of distantly related sequences von Prlić, Andreas, Domingues, Francisco S., Sippl, Manfred J.

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Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package von Tuncbag, Nurcan, Gosline, Sara J C, Kedaigle, Amanda, Soltis, Anthony R, Gitter, Anthony, Fraenkel, Ernest

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Getting more out of biomedical documents with GATE's full lifecycle open source text analytics von Cunningham, Hamish, Tablan, Valentin, Roberts, Angus, Bontcheva, Kalina

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VBA: a probabilistic treatment of nonlinear models for neurobiological and behavioural data von Daunizeau, Jean, Adam, Vincent, Rigoux, Lionel

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OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis von Finak, Greg, Frelinger, Jacob, Jiang, Wenxin, Newell, Evan W, Ramey, John, Davis, Mark M, Kalams, Spyros A, De Rosa, Stephen C, Gottardo, Raphael

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Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist von Drawert, Brian, Hellander, Andreas, Bales, Ben, Banerjee, Debjani, Bellesia, Giovanni, Daigle, Jr, Bernie J, Douglas, Geoffrey, Gu, Mengyuan, Gupta, Anand, Hellander, Stefan, Horuk, Chris, Nath, Dibyendu, Takkar, Aviral, Wu, Sheng, Lötstedt, Per, Krintz, Chandra, Petzold, Linda R

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Wham: Identifying Structural Variants of Biological Consequence von Kronenberg, Zev N, Osborne, Edward J, Cone, Kelsey R, Kennedy, Brett J, Domyan, Eric T, Shapiro, Michael D, Elde, Nels C, Yandell, Mark

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Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology von Medley, J Kyle, Choi, Kiri, König, Matthias, Smith, Lucian, Gu, Stanley, Hellerstein, Joseph, Sealfon, Stuart C, Sauro, Herbert M

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CeleST: computer vision software for quantitative analysis of C. elegans swim behavior reveals novel features of locomotion von Restif, Christophe, Ibáñez-Ventoso, Carolina, Vora, Mehul M, Guo, Suzhen, Metaxas, Dimitris, Driscoll, Monica

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